ICML 2025 Papers

Conformal prediction is a powerful tool for constructing prediction intervals for black-box models, providing a finite sample coverage guarantee for exchangeable data. However, this exchangeability is compromised when some entries of the test feature are contaminated, such as in the case of cellwise outliers. To address this issue, this paper introduces a novel framework called *detect-then-impute conformal prediction*. This framework first employs an outlier detection procedure on the test feature and then utilizes an imputation method to fill in those cells identified as outliers. To quantify the uncertainty in the processed test feature, we adaptively apply the detection and imputation procedures to the calibration set, thereby constructing exchangeable features for the conformal prediction interval of the test label. We develop two practical algorithms, $\texttt{PDI-CP}$ and $\texttt{JDI-CP}$, and provide a distribution-free coverage analysis under some commonly used detection and imputation procedures. Notably, $\texttt{JDI-CP}$ achieves a finite sample $1-2\alpha$ coverage guarantee. Numerical experiments on both synthetic and real datasets demonstrate that our proposed algorithms exhibit robust coverage properties and comparable efficiency to the oracle baseline.

Quality statistical inference requires a sufficient amount of data, which can be missing or hard to obtain. To this end, prediction-powered inference has risen as a promising methodology, but existing approaches are largely limited to Z-estimation problems such as inference of means and quantiles. In this paper, we apply ideas of prediction-powered inference to e-values. By doing so, we inherit all the usual benefits of e-values -- such as anytime-validity, post-hoc validity and versatile sequential inference -- as well as greatly expand the set of inferences achievable in a prediction-powered manner. In particular, we show that every inference procedure that can be framed in terms of e-values has a prediction-powered counterpart, given by our method. We showcase the effectiveness of our framework across a wide range of inference tasks, from simple hypothesis testing and confidence intervals to more involved procedures for change-point detection and causal discovery, which were out of reach of previous techniques. Our approach is modular and easily integrable into existing algorithms, making it a compelling choice for practical applications.

Handling missing values at test time is challenging for machine learning models, especially when aiming for both high accuracy and interpretability. Established approaches often add bias through imputation or excessive model complexity via missingness indicators. Moreover, either method can obscure interpretability, making it harder to understand how the model utilizes the observed variables in predictions. We propose *missingness-avoiding* (MA) machine learning, a general framework for training models to rarely require the values of missing (or imputed) features at test time. We create tailored MA learning algorithms for decision trees, tree ensembles, and sparse linear models by incorporating classifier-specific regularization terms in their learning objectives. The tree-based models leverage contextual missingness by reducing reliance on missing values based on the observed context. Experiments on real-world datasets demonstrate that **MA-DT, MA-LASSO, MA-RF**, and **MA-GBT** effectively reduce the reliance on features with missing values while maintaining predictive performance competitive with their unregularized counterparts. This shows that our framework gives practitioners a powerful tool to maintain interpretability in predictions with test-time missing values.

Conformal Prediction is a widely studied technique to construct prediction sets of future observations. Most conformal prediction methods focus on achieving the necessary coverage guarantees, but do not provide formal guarantees on the size (volume) of the prediction sets. We first prove the impossibility of volume optimality where any distribution-free method can only find a trivial solution. We then introduce a new notion of volume optimality by restricting the prediction sets to belong to a set family (of finite VC-dimension), specifically a union of $k$-intervals. Our main contribution is an efficient distribution-free algorithm based on dynamic programming (DP) to find a union of $k$-intervals that is guaranteed for any distribution to have near-optimal volume among all unions of $k$-intervals satisfying the desired coverage property. By adopting the framework of distributional conformal prediction (Chernozhukov et al., 2021), the new DP based conformity score can also be applied to achieve approximate conditional coverage and conditional restricted volume optimality, as long as a reasonable estimator of the conditional CDF is available. While the theoretical results already establish volume-optimality guarantees, they are complemented by experiments that demonstrate that our method can significantly outperform existing methods in many settings.

Conformal Prediction (CP) is a principled framework for quantifying uncertainty in black-box learning models, by constructing prediction sets with finite-sample coverage guarantees. Traditional approaches rely on scalar nonconformity scores, which fail to fully exploit the geometric structure of multivariate outputs, such as in multi-output regression or multiclass classification. Recent methods addressing this limitation impose predefined convex shapes for the prediction sets, potentially misaligning with the intrinsic data geometry. We introduce a novel CP procedure handling multivariate score functions through the lens of optimal transport. Specifically, we leverage Monge-Kantorovich vector ranks and quantiles to construct prediction region with flexible, potentially non-convex shapes, better suited to the complex uncertainty patterns encountered in multivariate learning tasks. We prove that our approach ensures finite-sample, distribution-free coverage properties, similar to typical CP methods. We then adapt our method for multi-output regression and multiclass classification, and also propose simple adjustments to generate adaptive prediction regions with asymptotic conditional coverage guarantees. Finally, we evaluate our method on practical regression and classification problems, illustrating its advantages in terms of (conditional) coverage and efficiency.

Recent advances in lightweight time series forecasting models suggest the inherent simplicity of time series forecasting tasks. In this paper, we present CMoS, a super-lightweight time series forecasting model. Instead of learning the embedding of the shapes, CMoS directly models the spatial correlations between different time series chunks. Additionally, we introduce a Correlation Mixing technique that enables the model to capture diverse spatial correlations with minimal parameters, and an optional Periodicity Injection technique to ensure faster convergence. Despite utilizing as low as 1% of the lightweight model DLinear's parameters count, experimental results demonstrate that CMoS outperforms existing state-of-the-art models across multiple datasets. Furthermore, the learned weights of CMoS exhibit great interpretability, providing practitioners with valuable insights into temporal structures within specific application scenarios.

Peptide sequencing—the process of identifying amino acid sequences from mass spectrometry data—is a fundamental task in proteomics. Non-Autoregressive Transformers (NATs) have proven highly effective for this task, outperforming traditional methods. Unlike autoregressive models, which generate tokens sequentially, NATs predict all positions simultaneously, leveraging bidirectional context through unmasked self-attention. However, existing NAT approaches often rely on Connectionist Temporal Classification (CTC) loss, which presents significant optimization challenges due to CTC's complexity and increases the risk of training failures. To address these issues, we propose an improved non-autoregressive peptide sequencing model that incorporates a structured protein sequence curriculum learning strategy. This approach adjusts protein's learning difficulty based on the model’s estimated protein generational capabilities through a sampling process, progressively learning peptide generation from simple to complex sequences. Additionally, we introduce a self-refining inference-time module that iteratively enhances predictions using learned NAT token embeddings, improving sequence accuracy at a fine-grained level. Our curriculum learning strategy reduces NAT training failures frequency by more than 90% based on sampled training over various data distributions. Evaluations on nine benchmark species demonstrate that our approach outperforms all previous methods across multiple metrics and species. Model and source code are available at https://github.com/BEAM-Labs/denovo.

A fundamental question in data-driven decision making is how to quantify the uncertainty of predictions to inform risk-sensitive downstream actions, as often required in domains such as medicine. We develop a decision-theoretic foundation linking prediction sets to risk-averse decision-making, addressing three questions: (1) What is the correct notion of uncertainty quantification for risk-averse decision makers? We prove that prediction sets are optimal for decision makers who wish to optimize their value at risk. (2) What is the optimal policy that a risk averse decision maker should use to map prediction sets to actions? We show that a simple max-min decision policy is optimal for risk-averse decision makers. Finally, (3) How can we derive prediction sets that are optimal for such decision makers? We provide an exact characterization in the population regime and a distribution free finite-sample construction. These insights leads to *Risk-Averse Calibration (RAC)*, a principled algorithm that is both *practical*—exploiting black-box predictions to enhance downstream utility—and *safe*—adhering to user-defined risk thresholds. We experimentally demonstrate RAC's advantages in medical diagnosis and recommendation systems, showing that it substantially improves the trade-off between safety and utility, delivering higher utility than existing methods while avoiding critical errors.

We present a new method for generating confidence sets within the split conformal prediction framework. Our method performs a trainable transformation of any given conformity score to improve conditional coverage while ensuring exact marginal coverage. The transformation is based on an estimate of the conditional quantile of conformity scores. The resulting method is particularly beneficial for constructing adaptive confidence sets in multi-output problems where standard conformal quantile regression approaches have limited applicability. We develop a theoretical bound that captures the influence of the accuracy of the quantile estimate on the approximate conditional validity, unlike classical bounds for conformal prediction methods that only offer marginal coverage. We experimentally show that our method is highly adaptive to the local data structure and outperforms existing methods in terms of conditional coverage, improving the reliability of statistical inference in various applications.

As machine learning-based prediction systems are increasingly used in high-stakes situations, it is important to understand how such predictive models will perform upon deployment. Distribution-free uncertainty quantification techniques such as conformal prediction provide guarantees about the loss black-box models will incur even when the details of the models are hidden. However, such methods are based on frequentist probability, which unduly limits their applicability. We revisit the central aspects of conformal prediction from a Bayesian perspective and thereby illuminate the shortcomings of frequentist guarantees. We propose a practical alternative based on Bayesian quadrature that provides interpretable guarantees and offers a richer representation of the likely range of losses to be observed at test time.

Conformal prediction (CP) is a promising uncertainty quantification framework which works as a wrapper around a black-box classifier to construct prediction sets (i.e., subset of candidate classes) with provable guarantees. However, standard calibration methods for CP tend to produce large prediction sets which makes them less useful in practice. This paper considers the problem of integrating conformal principles into the training process of deep classifiers to directly minimize the size of prediction sets. We formulate conformal training as a bilevel optimization problem and propose the {\em Direct Prediction Set Minimization (DPSM)} algorithm to solve it. The key insight behind DPSM is to minimize a measure of the prediction set size (upper level) that is conditioned on the learned quantile of conformity scores (lower level). We analyze that DPSM has a learning bound of $O(1/\sqrt{n})$ (with $n$ training samples), while prior conformal training methods based on stochastic approximation for the quantile has a bound of $\Omega(1/s)$ (with batch size $s$ and typically $s \ll \sqrt{n}$). Experiments on various benchmark datasets and deep models show that DPSM significantly outperforms the best prior conformal training baseline with $20.46\\%\downarrow$ in the prediction set size and validates our theory.

Split Conformal Prediction (SCP) provides a computationally efficient way to construct confidence intervals in prediction problems. Notably, most of the theory built around SCP is focused on the single test point setting. In real-life, inference sets consist of multiple points, which raises the question of coverage guarantees for many points simultaneously. While *on average*, the False Coverage Proportion (FCP) remains controlled, it can fluctuate strongly around its mean, the False Coverage Rate (FCR). We observe that when a dataset is split multiple times, classical SCP may not control the FCP in a majority of the splits. We propose CoJER, a novel method that achieves sharp FCP control in probability for conformal prediction, based on a recent characterization of the distribution of conformal $p$-values in a transductive setting. This procedure incorporates an aggregation scheme which provides robustness with respect to modeling choices. We show through extensive real data experiments that CoJER provides FCP control while standard SCP does not. Furthermore, CoJER yields shorter intervals than the *state-of-the-art method* for FCP control and only slightly larger intervals than standard SCP.

As deep learning continues to be driven by ever-larger datasets, understanding which examples are most important for generalization has become a critical question. While progress in data selection continues, emerging applications require studying this problem in dynamic contexts. To bridge this gap, we pose the Incremental Data Selection (IDS) problem, where examples arrive as a continuous stream, and need to be selected without access to the full data source. In this setting, the learner must incrementally build a training dataset of predefined size while simultaneously learning the underlying task. We find that in IDS, the impact of a new sample on the model state depends fundamentally on both its geometric relationship in the feature space and its prediction error. Leveraging this insight, we propose PEAKS (Prediction Error Anchored by Kernel Similarity), an efficient data selection method tailored for IDS. Our comprehensive evaluations demonstrate that PEAKS consistently outperforms existing selection strategies. Furthermore, PEAKS yields increasingly better performance returns than random selection as training data size grows on real-world datasets. The code is available at https://github.com/BurakGurbuz97/PEAKS.

Accurate predictions rely on the expressiveness power of graph deep learning frameworks like graph neural networks and graph transformers, where a positional encoding mechanism has become much more indispensable in recent state-of-the-art (SOTA) works to record the canonical position information. However, the current positional encoding limits in three aspects, at least: (1) most positional encodings are pre-defined, and fixed functions, which are inadequate to adapt to the complex attributed graphs; (2) a few pioneering works propose the learnable positional encoding but still limited to the structural information, leaving the real-world time-evolving topological and feature information untouched; (3) most positional encodings should be equipped with transformer's attention mechanism to fully release the power, where the dense or relational attention is often unaffordable on large-scale structured data. Hence, we study the possibility of Learnable Spatial-Temporal Positional Encoding in an effective and efficient manner and then propose a simple temporal link prediction model named L-STEP. Briefly, for L-STEP, we (1) prove the proposed positional learning scheme can preserve the graph property from the spatial-temporal spectral viewpoint, (2) verify that MLPs can fully exploit the expressiveness and reach Transformers' performance on that encoding, (3) change different initial positional encoding inputs to show robustness, (4) analyze the theoretical complexity and obtain less empirical running time than SOTA, and (5) demonstrate its temporal link prediction out-performance on 13 classic datasets and with 10 algorithms in both transductive and inductive settings using 3 different sampling strategies. Also, L-STEP obtains the leading performance in the newest large-scale TGB benchmark.

Prediction-powered inference (PPI) enables valid statistical inference by combining experimental data with machine learning predictions. When a sufficient number of high-quality predictions is available, PPI results in more accurate estimates and tighter confidence intervals than traditional methods. In this paper, we propose to inform the PPI framework with prior knowledge on the quality of the predictions. The resulting method, which we call frequentist, assisted by Bayes, PPI (FAB-PPI), improves over PPI when the observed prediction quality is likely under the prior, while maintaining its frequentist guarantees. Furthermore, when using heavy-tailed priors, FAB-PPI adaptively reverts to standard PPI in low prior probability regions. We demonstrate the benefits of FAB-PPI in real and synthetic examples.

Large Language Models (LLMs) are discovered to suffer from accurately retrieving key information. To address this, we propose Mask-Enhanced Autoregressive Prediction (MEAP), a simple yet effective training paradigm that seamlessly integrates Masked Language Modeling (MLM) into Next-Token Prediction (NTP) to enhance the latter's in-context retrieval capabilities. Specifically, MEAP first randomly masks a small fraction of input tokens and then directly performs the standard next-token prediction autoregressive using a decoder-only Transformer. MEAP eliminates the need for bidirectional attention or encoder-decoder architectures for MLM, incurring no additional computational overhead during pre-training or inference. Intensive experiments demonstrate that MEAP substantially outperforms NTP on key information retrieval and long-context reasoning tasks, while performing on par or better on commonsense reasoning tasks. The benefits of MEAP also extend to supervised fine-tuning, where it shows remarkable advantages in lost-in-the-middle scenarios, outperforming NTP by 11.77% percentage points. Our analysis indicates that MEAP’s effectiveness arises from its ability to promote more distinguishable attention scores by concentrating on a reduced set of non-masked tokens. This mechanism improves the model’s focus on task-relevant signals while mitigating the influence of peripheral context. These findings position MEAP as a promising training paradigm for large language models. Code has been submitted.

Training neural networks on randomly generated artificial datasets yields Bayesian models that capture the prior defined by the dataset-generating distribution. Prior-data Fitted Networks (PFNs) are a class of methods designed to leverage this insight. In an era of rapidly increasing computational resources for pre-training and a near stagnation in the generation of new real-world data in many applications, PFNs are poised to play a more important role across a wide range of applications. They enable the efficient allocation of pre-training compute to low-data scenarios. Originally applied to small Bayesian modeling tasks, the field of PFNs has significantly expanded to address more complex domains and larger datasets. This position paper argues that PFNs and other amortized inference approaches represent the future of Bayesian inference, leveraging amortized learning to tackle data-scarce problems. We thus believe they are a fruitful area of research. In this position paper, we explore their potential and directions to address their current limitations.

Prediction-Powered Inference (PPI) is a powerful framework for enhancing statistical estimates by combining limited gold-standard data with machine learning (ML) predictions. While prior work has demonstrated PPI’s benefits for individual statistical problems, modern applications require answering numerous parallel statistical questions. We introduce Prediction-Powered Adaptive Shrinkage ($\texttt{PAS}$), a method that bridges PPI with empirical Bayes shrinkage to improve estimation of multiple means. $\texttt{PAS}$ debiases noisy ML predictions $\textit{within}$ each task and then borrows strength $\textit{across}$ tasks by using those same predictions as a reference point for shrinkage. The amount of shrinkage is determined by minimizing an unbiased estimate of risk, and we prove that this tuning strategy is asymptotically optimal. Experiments on both synthetic and real-world datasets show that $\texttt{PAS}$ adapts to the reliability of the ML predictions and outperforms traditional and modern baselines in large-scale applications.